He was nerfed cause a lot of people complained about him being too strong (which, to be honest, they were a right about, since he did damage that is hard to match even with very high level ninjas with good buffs).

Ironically the people that complained the most were F2P.
Tobi was easily upgradable to 5 stars by a F2P, and he basically was one of the few viable counters to the current high level top tier ninja's. Tobi was capable of one-shotting people with just his mistery and chase, given decent buffs. He could have been a good counter to immortal teams, by providing a quick way of killing tsunade, water main and sakura. He could have been a good counter to 6 Tails Naruto, cause tobi would have evaded his mistery every time, and could have done massive damage to him. He would have been good against a lot of ninjas. But hey, that was the choice of the majority...What can you do?
¯\(ツ)/¯

But basically, the F2P kicked themselves in the nuts with this. Sorry to say it, but it's the truth. He was broken indeed, but he was a powerful ninja and he was in everyone's reach.

Of course they won't nerf overpriced ninja. Cause they need people to drool at them and pay money for them. :P